scope.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: scope.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 19:23:36  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.107
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: scope.cpp,v 1000.5 2004/06/01 19:23:36 gouriano Exp $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Authors:
*           Andrei Gourianov
*           Aleksey Grichenko
*           Michael Kimelman
*           Denis Vakatov
*           Eugene Vasilchenko
*
* File Description:
*           Scope is top-level object available to a client.
*           Its purpose is to define a scope of visibility and reference
*           resolution and provide access to the bio sequence data
*
*/

#include <ncbi_pch.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/seq_annot_handle.hpp>
#include <objmgr/bioseq_set_handle.hpp>
#include <objmgr/impl/scope_impl.hpp>
#include <objmgr/impl/synonyms.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


/////////////////////////////////////////////////////////////////////////////
//
// CScope
//
/////////////////////////////////////////////////////////////////////////////


CScope::CScope(CObjectManager& objmgr)
{
    if ( CanBeDeleted() ) {
        // this CScope object is allocated in heap
        m_Impl.Reset(new CScope_Impl(objmgr));
        m_Impl->m_HeapScope = this;
    }
    else {
        // allocate heap CScope object
        m_HeapScope.Reset(new CScope(objmgr));
        _ASSERT(m_HeapScope->CanBeDeleted());
        m_Impl = m_HeapScope->m_Impl;
        _ASSERT(m_Impl);
    }
}


CScope::~CScope(void)
{
    if ( bool(m_Impl) && m_Impl->m_HeapScope == this ) {
        m_Impl->m_HeapScope = 0;
    }
}


CBioseq_Handle CScope::GetBioseqHandle(const CSeq_id& id)
{
    return m_Impl->GetBioseqHandle(id, eGetBioseq_All);
}


CBioseq_Handle CScope::GetBioseqHandle(const CSeq_id_Handle& id)
{
    return m_Impl->GetBioseqHandle(id, eGetBioseq_All);
}


CBioseq_Handle CScope::GetBioseqHandle(const CSeq_loc& loc)
{
    return m_Impl->GetBioseqHandle(loc, eGetBioseq_All);
}


CBioseq_Handle CScope::GetBioseqHandle(const CBioseq& seq)
{
    //ERR_POST_ONCE(Warning<<"CScope::GetBioseqHandle(CBioseq&) is deprecated");
    return m_Impl->GetBioseqHandle(seq);
}


CBioseq_Handle CScope::GetBioseqHandle(const CSeq_id& id,
                                       EGetBioseqFlag get_flag)
{
    return m_Impl->GetBioseqHandle(id, get_flag);
}


CBioseq_Handle CScope::GetBioseqHandle(const CSeq_id_Handle& id,
                                       EGetBioseqFlag get_flag)
{
    return m_Impl->GetBioseqHandle(id, get_flag);
}


CSeq_entry_Handle CScope::GetSeq_entryHandle(const CSeq_entry& entry)
{
    //ERR_POST_ONCE(Warning<<"CScope::GetSeq_entryHandle(CSeq_entry&) is deprecated.");
    return m_Impl->GetSeq_entryHandle(entry);
}


CSeq_annot_Handle CScope::GetSeq_annotHandle(const CSeq_annot& annot)
{
    //ERR_POST_ONCE(Warning<<"CScope::GetSeq_annotHandle(CSeq_annot&) is deprecated.");
    return m_Impl->GetSeq_annotHandle(annot);
}


CBioseq_Handle CScope::GetBioseqHandleFromTSE(const CSeq_id& id,
                                              const CBioseq_Handle& bh)
{
    return m_Impl->GetBioseqHandleFromTSE(id, bh);
}


CBioseq_Handle CScope::GetBioseqHandleFromTSE(const CSeq_id& id,
                                              const CSeq_entry_Handle& seh)
{
    return m_Impl->GetBioseqHandleFromTSE(id, seh);
}


CBioseq_Handle CScope::GetBioseqHandleFromTSE(const CSeq_id_Handle& id,
                                              const CBioseq_Handle& bh)
{
    return m_Impl->GetBioseqHandleFromTSE(id, bh);
}


CBioseq_Handle CScope::GetBioseqHandleFromTSE(const CSeq_id_Handle& id,
                                              const CSeq_entry_Handle& seh)
{
    return m_Impl->GetBioseqHandleFromTSE(id, seh);
}


void CScope::GetAllTSEs(TTSE_Handles& tses, enum ETSEKind kind)
{
    m_Impl->GetAllTSEs(tses, int(kind));
}


CBioseq_EditHandle CScope::GetEditHandle(const CBioseq_Handle& seq)
{
    return m_Impl->GetEditHandle(seq);
}


CSeq_entry_EditHandle CScope::GetEditHandle(const CSeq_entry_Handle& entry)
{
    return m_Impl->GetEditHandle(entry);
}


CSeq_annot_EditHandle CScope::GetEditHandle(const CSeq_annot_Handle& annot)
{
    return m_Impl->GetEditHandle(annot);
}


CBioseq_set_EditHandle CScope::GetEditHandle(const CBioseq_set_Handle& seqset)
{
    return m_Impl->GetEditHandle(seqset);
}


void CScope::ResetHistory(void)
{
    m_Impl->ResetHistory();
}


CConstRef<CSynonymsSet> CScope::GetSynonyms(const CSeq_id& id)
{
    return m_Impl->GetSynonyms(id);
}


CConstRef<CSynonymsSet> CScope::GetSynonyms(const CSeq_id_Handle& id)
{
    return m_Impl->GetSynonyms(id);
}


CConstRef<CSynonymsSet> CScope::GetSynonyms(const CBioseq_Handle& bh)
{
    return m_Impl->GetSynonyms(bh);
}


void CScope::AddDefaults(TPriority priority)
{
    m_Impl->AddDefaults(priority);
}


void CScope::AddDataLoader(const string& loader_name, TPriority priority)
{
    m_Impl->AddDataLoader(loader_name, priority);
}


void CScope::AddScope(CScope& scope, TPriority priority)
{
    m_Impl->AddScope(*scope.m_Impl, priority);
}


CSeq_entry_Handle CScope::AddTopLevelSeqEntry(CSeq_entry& top_entry,
                                              TPriority priority)
{
    return m_Impl->AddTopLevelSeqEntry(top_entry, priority);
}


CBioseq_Handle CScope::AddBioseq(CBioseq& bioseq, TPriority priority)
{
    return m_Impl->AddBioseq(bioseq, priority);
}


CBioseq_Handle CScope::GetBioseqHandleFromTSE(const CSeq_id& id,
                                              const CSeq_entry& tse)
{
    //ERR_POST_ONCE(Warning<<"GetBioseqHandleFromTSE(CSeq_entry) is deprecated: use handles.");
    return GetBioseqHandleFromTSE(id, GetSeq_entryHandle(tse));
}


CBioseq_Handle CScope::GetBioseqHandleFromTSE(const CSeq_id_Handle& id,
                                              const CSeq_entry& tse)
{
    //ERR_POST_ONCE(Warning<<"GetBioseqHandleFromTSE(CSeq_entry) is deprecated: use handles.");
    return GetBioseqHandleFromTSE(id, GetSeq_entryHandle(tse));
}


void CScope::AttachEntry(CSeq_entry& parent, CSeq_entry& entry)
{
    //ERR_POST_ONCE(Warning<<"CScope::AttachEntry() is deprecated: use class CSeq_entry_EditHandle.");
    GetSeq_entryHandle(parent).GetSet().GetEditHandle().AttachEntry(entry);
}


void CScope::RemoveEntry(CSeq_entry& entry)
{
    //ERR_POST_ONCE(Warning<<"CScope::RemoveEntry() is deprecated: use class CSeq_entry_EditHandle.");
    GetSeq_entryHandle(entry).GetEditHandle().Remove();
}


void CScope::AttachAnnot(CSeq_entry& parent, CSeq_annot& annot)
{
    //ERR_POST_ONCE(Warning<<"CScope::AttachAnnot() is deprecated: use class CSeq_annot_EditHandle.");
    GetSeq_entryHandle(parent).GetEditHandle().AttachAnnot(annot);
}


void CScope::RemoveAnnot(CSeq_entry& parent, CSeq_annot& annot)
{
    //ERR_POST_ONCE(Warning<<"CScope::RemoveAnnot() is deprecated: use class CSeq_annot_EditHandle.");
    CSeq_entry_EditHandle eh = GetSeq_entryHandle(parent).GetEditHandle();
    CSeq_annot_EditHandle ah = GetSeq_annotHandle(annot).GetEditHandle();
    if ( ah.GetParentEntry() != eh ) {
        NCBI_THROW(CObjMgrException, eModifyDataError,
                   "CScope::RemoveAnnot: parent doesn't contain annot");
    }
    ah.Remove();
}


void CScope::ReplaceAnnot(CSeq_entry& parent,
                          CSeq_annot& old_annot, CSeq_annot& new_annot)
{
    //ERR_POST_ONCE(Warning<<"CScope::RemoveAnnot() is deprecated: use class CSeq_annot_EditHandle.");
    CSeq_entry_EditHandle eh = GetSeq_entryHandle(parent).GetEditHandle();
    CSeq_annot_EditHandle ah = GetSeq_annotHandle(old_annot).GetEditHandle();
    if ( ah.GetParentEntry() != eh ) {
        NCBI_THROW(CObjMgrException, eModifyDataError,
                   "CScope::ReplaceAnnot: parent doesn't contain old_annot");
    }
    ah.Remove();
    eh.AttachAnnot(new_annot);
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: scope.cpp,v $
* Revision 1000.5  2004/06/01 19:23:36  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.107
*
* Revision 1.107  2004/05/21 21:42:12  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.106  2004/04/13 15:59:35  grichenk
* Added CScope::GetBioseqHandle() with id resolving flag.
*
* Revision 1.105  2004/04/12 18:40:24  grichenk
* Added GetAllTSEs()
*
* Revision 1.104  2004/03/24 18:30:30  vasilche
* Fixed edit API.
* Every *_Info object has its own shallow copy of original object.
*
* Revision 1.103  2004/03/16 21:01:32  vasilche
* Added methods to move Bioseq withing Seq-entry
*
* Revision 1.102  2004/03/16 15:47:28  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.101  2004/02/19 17:23:01  vasilche